The way I see it as of now - I might as well have users like my facebook page since it will in effect from a user's perspective like my website but generate likes specifically for my facebook page which I will have regardless of whether or not I have a Like button for my website's URL.

This is a question about social media strategy not UX.
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dnbrvFeb 2 '12 at 12:11

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@dnbrv It's not a question about social media strategy; OP clearly is concerned with how his decision will affect his users. If it were "which one should I use to best market my product", then it would be social media strategy. As it is this is a great question for UX.
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Rahul♦Feb 2 '12 at 12:50

4 Answers
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If the user "likes" your web site (or even better, one of the articles on your web site), this is a one time action. As an effect, the user will post an "I like this page/article" on their wall and all their friends (or whatever publicity they choose) will see that post in their Facebook timeline. Then it will vanish into eternity... You will have no more interaction opportunity with this user.

If the user "likes" your Facebook page, then he will become a permanent fan of your page, and thus "receive" every post you make on your Facebook page in his timeline. So this "likes" scenario might have a narrow audience, since this "like" action will only affect this single user, but you will have a better opportunity to provide this user with valuable information. And remember, if your Facebook post is good, then the user might share that post with his friends.

I usually suggest that the main website should invite the visitor to visit/like your Facebook page. All your blog articles should have a "like this article/page" option to provide an independent sharing of your content.

It's a matter of building a relationship with a particular user vs an opportunity to advertise to many.

Liking a facebook page effectively 'subscribes' them to your content. This means far better retention than simply bookmarking, and poses less barriers to existing FB users than adding your feed to an RSS reader or email list. But it's a relationship, and users typically resist this if there's any reason not to trust your service or organization (i.e. it's commercial). A key question to ask yourself is: is it clear to users that my future content will continue to have value? If you write content on a narrow range of topics, and confront themes across multiple posts, perhaps so.

Liking an article shares it. This makes an item appear in the users' friends' news feeds, with the article's headline, image and perhaps a copy snippet. This is a great way to gain exposure, especially when a title or headline is particularly evocative (or even downright controversial). But the effect is transient. Still, this is acceptable if your content isn't going to regularly help a single user.

Ultimately, which sorts of exposure you want depends on your context and your strategy. Some services might not gain much from long-term relationships; others need it to thrive and persist. Those are big questions about product strategy, and only you can answer them.

I used to work at a social media marketing agency, and the biggest issue we had was clearly delineating between Liking the website, and Liking a Facebook fan page. Often times people would assume they were Liking the fan page, when in fact they were Liking the website.

One way to avoid the confusion is to use the Facebook Like Box plugin. It's a recognizable interface, so it's more clear to users that they are Liking your fan page, they're just doing it on your website.